Articles by quantixed

Step By Step: recreating a volcano plot in R

June 16, 2023 | quantixed

We have an analysis routine for proteomics data written for IgorPro. One output is a volcano plot. These plots show the fold change in one sample compared to another and plot that against a p-value to estimate how reproducible any changes observed are. This post is not about that software, ...
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Yet Another Movie: IMDB Top 250 movies

April 29, 2023 | quantixed

I’m not a big movie person. Nonetheless I have a media library with quite a few films in and I wondered how many “films to see before you die”-type movies I had in the collection, and how many were missing. I used R to find the answers. I’...
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Probot: building a Mastodon bot

February 4, 2023 | quantixed

I have long admired albums2hear, a Twitter bot that posts albums. You can read a bit more about it here. There was no mastodon equivalent and so I decided to build one. You can follow the bot – currently called Albums Albums Albums (or AlbumsX3) – here. Idea behind the bot ... [Read more...]

Running Around: 2022 running dataviz in R

January 2, 2023 | quantixed

2022 was my best year for running to date. In 2021, my goal was to run 2021 km. For 2022, I wanted to see if I could run 2500 km and also to run 50 HM-or-more distance runs. I managed both and ended the year on a total of 2734 km. I also bagged two […]
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Twitcher II: tweet frequency and top tweets

December 26, 2022 | quantixed

Another post looking at Twitter data in R. It follows this one and this one. I wanted to look again at my tweeting frequency over the 12 years on Twitter, but this time do it in a calendar view. Something like a GitHub commit calendar would be perfect. I have used ...
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Any Time At All: tweet frequency around the clock

December 21, 2022 | quantixed

Please consider this a “supplementary analysis” to my previous post looking at the frequency of tweets from my personal account over the last 12 years. I was curious about what times I was active on Twitter (measured by when I tweeted). Others might be interested in a solution to look at ...
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Twitcher: tweet frequency over the years

December 18, 2022 | quantixed

At the time of writing, I have essentially left Twitter. It was a fun ride and without going into what’s happening there now, this is a good opportunity to look at my 12 years on the platform. Early in November, I downloaded my data and locked my Twitter account. This ...
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Form and File: estimating running form in R

November 5, 2022 | quantixed

There are lots of ways for runners and cyclists to analyse training data. A key question most fitness enthusiasts want to know is “how am I doing?”. “How you are doing” is referred to as form. Unsurprisingly, form can be estimated in many ways. One method is using training stress ...
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Pledging My Time V: analysing race results in R

September 12, 2022 | quantixed

It’s been a while since I posted a breakdown of half marathon times. The last time seems to have been 2018. I decided to give my old code a clean-up and quickly crunched the numbers from the 2022 Kenilworth Half Marathon. First, the results: Briefly, the code below reads in a ...
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The Package: learning how to build an R package

September 6, 2022 | quantixed

I recently made my first R package and was asked how I did it. The answer of course was: I searched, read, and stumbled around until it was done. But having gone through the process I figured it was worthwhile summarising what I did and what I found tricky. First ...
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Tracking: announcing new R package TrackMateR

September 5, 2022 | quantixed

A short post to announce TrackMateR, a new R package to analyse TrackMate XML outputs. Code Instructions Background TrackMate is a plug-in for ImageJ which ships with Fiji. It’s essential for single particle tracking work, particularly for microscopy movies. For example, tracking the movement of fluorescent vesicles inside cells. ... [Read more...]

Wordless Song: Benchmarking Wordle performance using R

January 5, 2022 | quantixed

A quick post about a puzzle called Wordle that is currently taking over the internet. It’s a mastermind-like game where the object is to guess an unknown 5-letter word. Puzzlers are encouraged to share their results after completing a puzzle. Here is an example for puzzle 192. So how do ...
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Target II: Monitoring a running goal in R

December 23, 2021 | quantixed

As 2021 draws to a close, it’s time to check back in on a previous post. As a recap, Garmin Connect offered four challenges to run 3 x 505 km and 1 x 505 km, one in each of the four quarters of 2021. Completing all four would mean running 2021 km in 2021. I […]
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Under The Same Name: Journal titles and band names

November 4, 2021 | quantixed

Some journals sound like they should be bands. Whereas some journal titles ARE in fact the same as band names. I wondered… how many journal titles are also band names. Let’s find out! The journals cited in PubMed could be downloaded as a text file from here. This list ... [Read more...]

Over and Over: Preprint revisions on bioRxiv

April 7, 2021 | quantixed

The aim of this post is to look at revisions of bioRxiv preprints. I’m interested how long preprint versions exist on bioRxiv. In other words: how long do revisions to preprints take? The data from bioRxiv is a complex dataset with many caveats as I’ll explain further down, ...
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Os Mutantes: an implausible naming system for SARS-CoV-2 mutants

February 27, 2021 | quantixed

The scientific response to the COVID-19 pandemic has been astounding. Aside from efforts to generate vaccines, the genomic surveillance of the virus has been truly remarkable. For example, the nextstrain project has sequence many SARS-CoV-2 genomes. In fact, the rapid identification of multiple new strains and mutations by diverse groups ...
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